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Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Abstract Background Stroke induces immune alterations such as impaired oxidative burst and reduced release of neutrophil extracellular traps (NETs). We hypothesised that key enzymes of these defence mechanisms may be altered in ischaemic stroke. Therefore, we analysed the intra- and extracellular amounts of myeloperoxidase (MPO) and neutrophil elastase (NE) in patient sera and granulocytes and monocytes. Because the autonomous nervous system is thought to mediate stroke-induced immune alterations, we also studied the influence of stress...

Additional file 7: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
A: Influence of r-tPA on cytokine production with PHA stimulation. Production of INF-γ, IL-2, -4, -5, -6, -9, -13, -17A, -17 F, -21, -22 and TNF-α in the supernatants of PBMCs after 72 h of incubation with r-tPA. PBMCs were stimulated with PHA to induce cytokine production. IL-10 was not induced in any of the conditions and is not shown. As an example, the data from PBMCs isolated from venous blood of healthy donors anticoagulated with EDTA...

Additional file 6: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Influence of r-tPA on MPO and NE. PBMCs of healthy donors were incubated with 0.5 or 1 μg/ml r-tPA for 4 h at 37 °C in 5% CO2. Afterwards, MPO and NE were measured intracellularly in granulocytes by flow cytometry (A, C), expressed in MFI, and in the supernatant using ELISA (B, D), expressed in ng/ml (n = 10). *p 

Additional file 5: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Influence of adrenaline, noradrenaline, dexamethasone and acetylcholine on mean NET area. Effect of in vitro administration of 1 × 10−7 M or 1 × 10−5 M adrenaline (A) and noradrenaline (B); 2.5 × 10−7 M or 2.5 × 10−6 M dexamethasone (C); and 5.5 × 10−6 M or 5.5 × 10−4 M acetylcholine (D) on NET area was tested. After incubation of blood of healthy donors with hormones and acetylcholine for 4 h at room temperature, neutrophils were isolated, and NETs were induced using PMA or fMLP or...

Additional file 4: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Influence of adrenaline, noradrenaline, dexamethasone and acetylcholine on NE and MPO release in vitro. NE and MPO-ELISA of supernatants of PBMCs (of healthy donors) treated with 1 × 10−7 M (low) or 1 × 10−5 M (high) adrenaline and noradrenaline; 2.5 × 10−7 M (low) or 2.5 × 10−6 M (high) dexamethasone; and 5.5 × 10−6 M (low) or 5.5 × 10−4 M (high) acetylcholine. If the data failed a Gaussian distribution test by the D‘agostino & Pearson omnibus normality test, the data were analysed by the...

Additional file 3: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Influence of adrenaline, noradrenaline, dexamethasone and acetylcholine on intracellular NE and MPO in vitro. A: Intracellular MPO of granulocytes and monocytes of healthy donors treated with adrenaline, noradrenaline, dexamethasone or acetylcholine (n = 10). The mean and SD ranges are given. B: Intracellular NE of granulocytes and monocytes treated with adrenaline, noradrenaline, dexamethasone or acetylcholine (n = 10). The mean and SD ranges are given. (PDF 2057 kb)

Additional file 2: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Monocytic intracellular expression (MFI) of NE and MPO per cell in stroke patients versus controls. Stroke patients were analysed and compared to healthy controls. MPO (A) and NE (B) were measured intracellularly in monocytes using flow cytometry and are expressed in MFI. MPO was measured on the day of stroke admission (d0) and on days 1, 3 and 5 after stroke (d1, d3, d5) (A; ncrtl = 14, nd0 = 14, nd1 = 18, nd3 = 14, nd5 = 16). NE was measured on day...

Additional file 1: of Ischaemic stroke and the recanalization drug tissue plasminogen activator interfere with antibacterial phagocyte function

Antje Vogelgesang, Claudia Lange, Lara Blümke, Georg Laage, Sarah Rümpel, Sönke Langner, Barbara Bröker, Alexander Dressel & Johanna Ruhnau
Netosis in an adult control. In vitro imaging of NETs forming neutrophils with representative images for one control subject. A brightfield image allowed quantification of total cells, SYTOX® Green allowed quantification of NETosis based on size of events and comparison of different stimuli. One representative example of the unstimulated and one PMA stimulated sample is shown. Fiji Software was used to measure NET area. Images of SYTOX® Green stained cells were taken with a Leica...

Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Abstract Background Sub-lethal heat treatment characterizes a transition zone of radiofrequency ablation (RFA) which explains hepatocellular carcinoma (HCC) residual cancer occurrence in this area after RFA treatment. The biochemistry of residual cancer cell recurrence is poorly understood, but long noncoding RNAs (lncRNAs) may have aberrant expression that is associated with diverse cancers. Thus, we measured lncRNA gene expression in sub-lethally heat-treated HCC cells using microarray. Method Differentially expressed lncRNA and mRNA were measured with an...

Additional file 9: Table S7. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Significant correlation of cytoscape network. (XLS 51 kb)

Additional file 8: Table S6. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Liver specific lncRNA analysis. (XLSX 349 kb)

Additional file 7: Table S5. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Classification and subgroup analysis of downregulated lncRNAs. (XLSX 92 kb)

Additional file 6: Table S4. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Classification and subgroup analysis of upregulated lncRNAs. (XLSX 206 kb)

Additional file 5: Table S3. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Significantly differentially expressed lncRNAs and mRNAs. (XLS 2545 kb)

Additional file 4: Table S2. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
mRNA qRT-PCR primers and product size. (DOCX 17 kb)

Additional file 3: Table S1. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
lncRNA qRT-PCR primers and product size. (DOCX 18 kb)

Additional file 2: Figure S2. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
cRNA amplification and labeling procedures (TIF 251 kb)

Additional file 1: Figure S1. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
RNA quality. ① and ⑧: DL2000 Marker; ②: Normal cultured HCC cells(The first repeat experiment); ③: sub-lethally heat-treated HCC cells(The first repeat experiment); ④Normal cultured HCC cells(The second repeat experiment); ⑤sub-lethally heat-treated HCC cells(The second repeat experiment); ⑥Normal cultured HCC cells(The third repeat experiment); ⑦ sub-lethally heat-treated HCC cells(The third repeat experiment); (TIF 1244 kb)

Additional file 14: Table S12. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Target pathway enrichment. (XLSX 107 kb)

Additional file 13: Table S11. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
Target GO enrichment. (XLSX 443 kb)

Characterization of background noise in capture-based targeted sequencing data

Gahee Park, Joo Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung Kim, Yeon Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Lee, Dae-Soon Son, Woong-Yang Park & Donghyun Park
Abstract Background Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred during specific steps of the capture-based targeted sequencing process. Results We removed most sequencing artifacts by filtering out low-quality bases and then analyze the remaining background noise. By recognizing...

Additional file 12: Table S10. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
N vs C pathway enrichment. (XLSX 351 kb)

Additional file 3: Figure S1. of Characterization of background noise in capture-based targeted sequencing data

Gahee Park, Joo Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung Kim, Yeon Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Lee, Dae-Soon Son, Woong-Yang Park & Donghyun Park
Single nucleotide polymorphism concordance between plasma and PBL DNA samples. Figure S2. The distribution of base quality scores from generated sequencing data. Figure S3. The proportion of consistent/inconsistent errors between paired reads 1 and 2. Figure S4. Background allele frequencies of 12 substitution classes. Figure S5. Mutagenic DNA lesions are associated with high DNA-shearing conditions. Figure S6. Background allele frequencies around the DNA break point. Figure S7. Normalized mononucleotide frequencies around the DNA break point....

Additional file 11: Table S9. of Long noncoding RNA expression profiles in sub-lethal heat-treated hepatoma carcinoma cells

Qingsong Deng, Shihan Chen, Chunchuan Fu, Jiayun Jiang, Mengda Zou, Yunhua Tan, Xiaofei Wang, Feng Xia, Kai Feng, Kuansheng Ma & Ping Bie
N vs C GO enrichment. (XLSX 1980 kb)

Additional file 2: Table S2. of Characterization of background noise in capture-based targeted sequencing data

Gahee Park, Joo Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung Kim, Yeon Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Lee, Dae-Soon Son, Woong-Yang Park & Donghyun Park
Genes targeted for massively parallel sequencing. Table S3. Summary of sequencing metrics for 19 paired plasma and PBL DNA samples. Table S4. Acoustic shearing conditions. Table S5. Donor characteristics and KRAS variant allele frequency. (XLSX 19 kb)

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